Introduction and Acknowledgements
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the NA-MIC website.
This program collects together three common image processing tasks that all involve resampling an image volume: Resampling to a new resolution and spacing, applying a transformation (using an ITK transform IO mechanisms) and Warping (using a vector image deformation field). Full documentation available here: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSResample.
Most frequently used for these scenarios:
- Change an image's resolution and spacing.
- Apply a transformation to an image (using an ITK transform IO mechanisms)
- Warping an image (using a vector image deformation field).
Links to tutorials that use this module
Panels and their use
- Inputs: Parameters for specifying the image to warp and resulting image space
- Image To Warp (inputVolume): Image To Warp
- Reference Image (referenceVolume): Reference image used only to define the output space. If not specified, the warping is done in the same space as the image to warp.
- Outputs: Resulting deformed image parameters
- Output Image (outputVolume): Resulting deformed image
- Pixel Type (pixelType): Specifies the pixel type for the input/output images. If the type is "input", then infer from the input image. The "binary" pixel type uses a modified algorithm whereby the image is read in as unsigned char, a signed distance map is created, signed distance map is resampled, and then a thresholded image of type unsigned char is written to disk.
- Warping Parameters: Parameters used to define home the image is warped
- Displacement Field (deprecated) (deformationVolume): Displacement Field to be used to warp the image (ITKv3 or earlier)
- Transform file (warpTransform): Filename for the BRAINSFit transform (ITKv3 or earlier) or composite transform file (ITKv4)
- Interpolation Mode (interpolationMode): Type of interpolation to be used when applying transform to moving volume. Options are Linear, ResampleInPlace, NearestNeighbor, BSpline, or WindowedSinc
- Compute inverse transform of given transformation? (inverseTransform): True/False is to compute inverse of given transformation. Default is false
- Default Value (defaultValue): Default voxel value
- Advanced Options:
- Add Grids (gridSpacing): Add warped grid to output image to help show the deformation that occured with specified spacing. A spacing of 0 in a dimension indicates that grid lines should be rendered to fall exactly (i.e. do not allow displacements off that plane). This is useful for makeing a 2D image of grid lines from the 3D space
- Multiprocessing Control:
- Number Of Threads (numberOfThreads): Explicitly specify the maximum number of threads to use.
- NearestNeighbor: The value of the nearest voxel is copied into the new voxel
- Linear: The average of the voxels in the input image occupying the new voxel volume is used
- ResampleInPlace: Detailed information can be found here
- BSpline: Detailed information can be found here
- WindowedSinc: Detailed information can be found here
Publications related to this module go here. Links to pdfs would be useful. For extensions: link to the source code repository and additional documentation
Information for Developers
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